Previous studies have suggested that unidentified compounds constitute a large proportion of extractable organochlorine (EOCl) and extractable organobromine (EOBr) in the crude extracts without fractionation; however, the proportion of unidentified EOX (X = chlorine, bromine) associated with high-/low-molecular-weight compounds is still unknown. In this study, we applied gel permeation chromatography to fractionate extracts from archived liver samples of high-trophic marine and terrestrial mammals (striped dolphins, cats, and raccoon dogs), for which concentrations of legacy organohalogen contaminants (polychlorinated biphenyls, organochlorine pesticides, and polybrominated diphenyl ethers [PBDEs]) had been previously reported. EOX in high- (>1000 g/mol) and low- (≤1000 g/mol) molecular-weight fractions (EOX-H and EOX-L) were determined by neutron activation analysis. Comparison of EOCl and EOBr enabled the characterization among species. Despite small differences in the concentrations and molecular-weight profiles of EOCl among species, the contribution of chlorine in identified compounds to EOCl-L varied from 1.5% (cats) to 79% (striped dolphins). Considerable species-specific variations were observed in the concentrations of EOBr: striped dolphins exhibited significantly greater concentrations of both EOBr-H and EOBr-L than cats and/or raccoon dogs. Moreover, the contribution of bromine in PBDEs to EOBr-L was >50% in two cats, while it was <6% in other specimens. This is the first report on EOBr mass balance in cetaceans and on EOX mass balance in terrestrial mammals living close to humans. These results suggest the need for analysis of unidentified chlorinated compounds in terrestrial mammals and unidentified brominated compounds in marine mammals.